(RNS) More than once in the past few months, The New York Times has lifted up a corner of the Catholic carpet and found all sorts of nasty things scurrying about.

In its coverage of the Catholic sex abuse scandal, the Gray Lady has zeroed in on Pope Benedict XVI’s role in processing abuse claims, first as Archbishop Joseph Ratzinger in Munich, then as Cardinal Ratzinger at the Vatican, and most recently as pope.

As its critical news stories about the abuse scandal reached a crescendo, here and there a cardinal or bishop spoke out; the pope said the larger church should not be “intimidated by the petty gossip of dominant opinion.”

New York Archbishop Timothy Dolan has complained that the Times has peddled an “anti-Catholic” bias. Times religion reporter Laurie Goodstein, in a letter to Dolan that later surfaced in the blogosphere, defended her work, telling Dolan, “I cannot accept your characterization of the Times as “anti-Catholic.”‘

The latest story from the Times, published on July 1, examines Benedict’s 23-year history as head of the Congregation for the Doctrine of the Faith, the Vatican office that assumed control of all abuse cases on Ratzinger’s watch. The story attempts to prove Benedict could have — or should have — done more.

But here’s the problem: While Ratzinger was head of the CDF, his hands were tied by the Vatican bureaucracy and his hear-no-evil see-no-evil boss, Pope John Paul II.

By the time the abuse scandal exploded in the U.S. in 2002, it was too late, and Ratzinger (and later, Benedict) was left to clean up the mess that John Paul had allowed to fester unchecked for years.

It’s an important distinction that the Times has yet to realize, including in the paper’s most recent story:

“The future pope, it is now clear, was also part of a culture of nonresponsibility, denial, legalistic foot-dragging and outright obstruction,” the Times wrote on July 1.

“More than any top Vatican official … it was Cardinal Ratzinger who might have taken decisive action in the 1990s to prevent the scandal from metastasizing in country after country, growing to such proportions that it now threatens to consume his own papacy.”

But there’s a larger problem here. The Times, and the church, are simply operating in two distinctly different universes.

“The Catholic Church is a hierarchical church,” Goodstein wrote to Dolan last fall, “with a clear chain of accountability.” That statement can be summarized in three short words: just plain wrong.

The Catholic Church is not a multi-national top-down organization with a CEO pope and a direct chain of command, like Citibank or General Electric. While the church appears to have a military-like structure, it functions more like a territorial franchise operation. The papacy coordinates more than it rules.

Considered the successor to St. Peter, the pope is bishop of Rome, and first among equals in relation to other bishops. Through his curial offices, he coordinates bishops’ efforts to stay “in communion” with Rome and each other, ensuring that bishops are following the letter of canon law and the spirit of church councils.

In other words, the papacy is far from a one-man show.

While each bishop ultimately reports to the pope, he is nonetheless responsible for everything that occurs in his diocese, and a lot of these bishops simply didn’t do what they were supposed to do. The ones that did were stymied by John Paul’s Vatican bureaucracy.

What’s a bishop to do with an abusive priest? Simple: fire him. Refuse to give him “faculties” (in essence, a license) to perform sacraments. No faculties means no assignment, and no assignment can mean no salary and no place to live.

Did some bishops hide creeps from the police and parishioners, perhaps because they did not “get it”? Yes. Was Benedict one of them? I’m not so sure. Will the Times pump more scandal into the air? Probably.

The story here is not what was, but what is and what will be.

Benedict gets it and we hope that the universal church — especially the curia — gets it. But the Times, for whatever reason, doesn’t.

(Phyllis Zagano is senior research associate-in-residence at Hofstra University and author of several books in Catholic Studies.)